Hey Chris,
Great work! I had run dotTrace myself and seen the same problem, but I hadn't had time to do anything about it.
I think there are a few places that could benefit from some parallelisation, but they may require some architectural changes. Particularly the phases of parsing the xml and assembly are both independent, but currently run in sequence; these could quite reasonably be run side-by-side.
Anyway, keep up the good work!
James